fix broken and inconsistent links in the manual

doc/src/Commands_bond.txt

@@ -95,7 +95,7 @@ OPT.
 "helix (o)"_dihedral_helix.html,
 "multi/harmonic (o)"_dihedral_multi_harmonic.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
-"opls (iko)"_dihedral_opls.htm;,
+"opls (iko)"_dihedral_opls.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
 "table (o)"_dihedral_table.html,

doc/src/Howto_spherical.txt

@@ -159,7 +159,7 @@ ellipsoidal particles:
 
 The advantage of these fixes is that those which thermostat the
 particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting.  The "fix langevin"_fix_langevin
+calculation and thermostatting.  The "fix langevin"_fix_langevin.html
 command can also be used with its {omgea} or {angmom} options to
 thermostat the rotational degrees of freedom for spherical or
 ellipsoidal particles.  Other thermostatting fixes only operate on the

doc/src/Packages_details.txt

@@ -297,7 +297,7 @@ lib/gpu/README
 "Section 2.6 -sf gpu"_Run_options.html
 "Section 2.6 -pk gpu"_Run_options.html
 "package gpu"_package.html
-"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
+"Commands all"_lc pages (pair,kspace) for styles followed by (g)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -412,7 +412,7 @@ lib/kokkos/README
 "Section 2.6 -sf kk"_Run_options.html
 "Section 2.6 -pk kokkos"_Run_options.html
 "package kokkos"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line
@@ -1392,7 +1392,7 @@ src/USER-INTEL/README
 "Section 2.6 -sf intel"_Run_options.html
 "Section 2.6 -pk intel"_Run_options.html
 "package intel"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
 src/USER-INTEL/TEST
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
@@ -1698,7 +1698,7 @@ src/USER-OMP/README
 "Section 2.6 -sf omp"_Run_options.html
 "Section 2.6 -pk omp"_Run_options.html
 "package omp"_package.html
-"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
+"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
 :line

doc/src/Python_call.txt

@@ -59,7 +59,7 @@ and callbacks to LAMMPS.
 The "fix python/invoke"_fix_python_invoke.html command can execute
 Python code at selected timesteps during a simulation run.
 
-The "pair_style python"_pair_python command allows you to define
+The "pair_style python"_pair_python.html command allows you to define
 pairwise potentials as python code which encodes a single pairwise
 interaction.  This is useful for rapid-developement and debugging of a
 new potential.

doc/src/Speed_intel.txt

@@ -400,7 +400,7 @@ within the input script to automatically append the "omp" suffix to
 styles when USER-INTEL styles are not available.
 
 NOTE: For simulations on higher node counts, add "processors * * * 
-grid numa"_processors.html" to the beginning of the input script for
+grid numa"_processors.html to the beginning of the input script for
 better scalability.
 
 When running on many nodes, performance might be better when using

doc/src/Speed_packages.txt

@@ -72,7 +72,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
 "pair_style lj/cut/opt"_pair_lj.html :ul
 
 To see what accelerate styles are currently available for a particular
-style, find the style name in the "Commands_all"_Commands_all.html
+style, find the style name in the "Commands_all"_lc
 style pages (fix,compute,pair,etc) and see what suffixes are listed
 (g,i,k,o,t) with it.  The doc pages for individual commands
 (e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list